Super Typhoon Doksuri was packing maximum sustained winds of 185 kilometres an hour (115 miles per hour) as it headed towards a group of three lightly populated islands off the northern tip of the main island of Luzon, the agency said.
The storm, which is called "Egay" in the Philippines, was expected to make landfall or pass very close to the Babuyan islands or northeastern Cagayan province by Wednesday afternoon, the agency said in its latest bulletin at 0000 GMT.
It would then sweep across to Taiwan and eastern China.
The storm was expected to dump more than 200 millimetres (7.9 inches) of rain on the islands and the northern portion of Cagayan, Apayao and Ilocos Norte provinces on Tuesday.
Three of the five Babuyan islands are inhabited, with a population of around 20,000 people.
Local disaster official Charles Castillejos said coastal communities on the islands had been ordered to leave their homes, while fishermen had been told to get their boats out of the water.
"We sent the police to convince the hard-headed ones who refuse to evacuate," Castillejos told AFP.
Storm surges of more than three metres (10 feet) could hit some low-lying areas, the weather agency warned.
Heavy rain was expected across the mountainous northern provinces in the coming days, with landslides "highly likely", it added.
The Philippines is hit by an average of 20 major storms each year that kill hundreds of people and keep vast regions in perpetual poverty.
Scientists have warned that such storms, which also kill livestock and destroy key infrastructure, are becoming more powerful as the world gets warmer because of climate change.
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